Misunderstanding
by everg8er23
Summary: Rodney feels uncomfortable when a Sheppard from an alternate reality appears in Atlantis and sits Rodney down for a little talk. Let the awkwardness commence! This is kind of a fake McShep fic, now I know you are curious.
1. Chapter 1

"**Misunderstanding"**

**Summary: Rodney feels uncomfortable when a Sheppard from an alternate reality appears in Atlantis and sits Rodney down for a little talk. McShep (sort of)?**

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Rodney McKay was walking down the corridor on his way to his quarters for what he hoped would be a very extended nap. He had not slept much in the past week and it showed in the dark circles under his eyes and in his mussed up hair. Once again a visitor from an alternate reality was wandering around Atlantis. This time it was Rodney's friend and team leader John Sheppard. From what they had learned from the other Sheppard his reality was very similar to their own. This made dealing with his presence much easier… or much harder depending on how you looked at it. It meant he knew pretty much all there was to know about this Atlantis and didn't need hand-holding when it came to finding his way around. However, it also meant that when they did find differences between the two universes they were much more shocking. And Rodney was in store for one of the biggest surprises yet.

"McKay, wait up!"

Rodney, upon hearing the voice, turned around to find Sheppard running to catch up with him. "What is it now?" He grumbled in his usual over dramatic way. He was sure that he was once again about to be deprived of the life-saving sleep that he was wishing for.

"I need to talk to you."

Sighing loudly, Rodney responded irritated, "Talk to me tomorrow." Then realizing he had no clue which Sheppard he was talking to (hey, they looked exactly the same), he asked, "Which one are you again?"

Although one might have expected Sheppard to be taken aback at the question he just said simply, "The other one." Apparently he had gotten that question quite a few times over the past couple days. Rodney had tried to petition for them both to be labeled clearly at all times, but Carter wouldn't agree to force them to wear name tags. So, Rodney had been forced into the disconcertingly uncomfortable position of figuring out which Sheppard he was actually talking to every time he had a conversation with one of them.

"I want to talk now."

McKay had been about to protest loudly when he caught the expression on Sheppard's face and decided that his sleep could wait a few more minutes. "Fine, go ahead."

"In private?" Sheppard asked.

Rodney scrutinized the man's face, but all he learned was that this Sheppard was as good as hiding his feelings as the other one was. Acquiescing to the abnormal request, Rodney led him into his quarters which they were practically standing in front of anyway. The tired scientist immediately collapsed onto his bed. Sheppard slouched down close to Rodney. Too close. They were practically touching elbows but Rodney was too tired to move. Several long uneasy minutes passed before Sheppard finally said, "I've wanted to talk to you about my universe for awhile. There are things I haven't told you, or anyone. But I should tell you, I owe it to you."

At this Rodney perked up slightly. Whatever Sheppard was about to reveal was clearly very important. He looked at the man next to him, what his mouth wasn't saying was being screamed at him from his eyes. He was looking at Rodney in a way the real Sheppard never did. Rodney suddenly felt very self conscious.

"I've been here for a week already and I'm finding myself…" Sheppard trailed off but instead of continuing, he grabbed Rodney's hand. "I miss you."

Rodney stiffened at the unexpected contact and felt his ears grow hot. Sheppard, ignoring Rodney's body language, plunged on. "I mean I miss my Rodney. But you two are just so alike. And the way you look at John, it's the way my Rodney looks at me. I know the John you know can be a bit thick at times. But I wanted to let you know that I've noticed."

At these words Rodney felt himself blushing even more furiously and Sheppard still hadn't let go of his hand. He desperately wanted to pull his hand away but was in shock at what he had just heard. Was Sheppard really insinuating that he was… That he… was batting for the other team? The thought made him want to laugh, but the way Sheppard was looking at him told him not to. "I think you're confused." Rodney started. This entire situation was too surreal to actually be happening right now. Was it possible that the lack of sleep was actually making him hallucinate? That seemed more plausible than sitting on his bed holding the hand of an alternate reality Sheppard who was clearly gay, and in a relationship with Rodney's own gay alternate self. Thinking about it he let out a snort, which he then tried to cover up by yawning hugely.

"Rodney, I'm not the one confused here." Sheppard was moving closer.

Taking his free hand, Rodney laid it on Sheppard's shoulder in an attempt to keep him where he was. Sheppard, however, read this differently and began stroking Rodney's hand with his thumb. Rodney pulled at his hand, but Sheppard held on and was again moving in closer. Before Rodney knew what had happened he felt lips on his own, then – SMACK! Rodney had slapped Sheppard in the face. He was standing up and on the other side of the room in an instant.

Sheppard looked momentarily stunned before realization dawned on his face, "Oh, you're not…?"

"Nope." Rodney said quickly as he crossed his arms protectively over his chest.

"Oh." A pause. "Sorry, it's just that the way you look at…" Sheppard fidgeted with his hands.

Needing to fill the awkward silence Rodney said, "So you and your Rodney you…" He waved his finger as if gesturing between Sheppard and a non-existent person.

"Yeah, for about a year." Sheppard was now the one turning red.

"How's that?" Rodney tried to sound casual, but his voice came out rather higher than normal.

Sheppard had still not looked at him, "It's good. You're, I mean… he is really good at…"

"Oh, that's good." Rodney really didn't want Sheppard to finish that sentence. As it was he was picturing things he'd really rather not.

"I was going to say, he's good at listening." Sheppard finally met Rodney's eyes with an all too familiar smirk spread across his face.

"Right." Rodney said lamely.

Sheppard stood, again fidgeting with his hands. "Well, I'll be going then." He said at last and headed for the door.

"Wait, how do I look at John?" Rodney kicked himself even as he said it. Sheppard smiled, his eyes twinkling. "You know what, don't answer that."

"Goodnight Rodney."

As the other Sheppard left the room Rodney was left to wonder why, as a straight man, he always wound up kissing other men against his will.

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**A/N: I've planned this little piece as a one-shot, but if there's enough response I'm considering doing another chapter in which Rodney tells the real Sheppard about all of this. What do you guys think?**


	2. Chapter 2

**A/N: Thanks so much for all the words of encouragement. Thanks especially to jackrocks for pointing out something I should have noticed. I have addressed that little fact in here. So without further ado, here is the next installment.**

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"Well um, I'd say I hate to see you go, but one Sheppard is more than enough for me." Rodney was standing in one of the science labs. In front of him was the other Sheppard who was clearly more than ready to go home. After spending three days actively avoiding the man, Rodney was also anxious for the man to be leaving. "Not that having you around wasn't ah, interesting." He colored slightly, recalling a certain past event.

"I sure am going to miss you." The 'real' John Sheppard clapped his alternate self on the shoulder. "You always listen to reason; you're easy to get along with, not to mention you aren't bad looking."

Rodney's faced flushed even more as Sheppard said this last part, but he still managed to get in a snide comment about how cocky pilots could be.

"I could say the same things about you, John." The other Sheppard replied grinning from ear to ear.

"You're sure this thing is safe?" Sheppard asked eyeing the mass of electronic equipment, which even to an untrained eye looked jury rigged.

The other Sheppard just chuckled, "I have the utmost faith in you, Rodney." He gave Rodney a look which caused the scientist to squirm uncomfortably, but the Sheppard that belonged in this universe was too busy inspecting the device to notice.

"Um, right. Yeah." McKay told his shoes as he scuffed one against the other. Boy was he going to be glad when the alternate Sheppard was no longer around. How uncomfortable the other man made Rodney feel was the main reason he had been pushing himself so hard the past few days in order to figure out how to send him back home. As it turned out his persistence had paid off in the end, allowing him to come up with an ingenious solution which, while it would only work once, was certainly clever enough to earn the Nobel Prize, that was if anyone ever found out about it.

"Alright, well I guess it's time to go." The other Sheppard shot Rodney a pointed look.

"Oh yes, right." Rodney turned to one of the many laptops set up in the area. "Initializing quantum flux reactor now." He tapped the enter key. A soft mechanical noise began to issue from the dubious looking device. Suddenly a small hole appeared in the middle of the room. At least it looked like a hole at first. It expanded quickly, forming a circular, swirling aperture that was glowing intensely with energy. The three men shielded their eyes until the aperture dimmed slightly.

"I think I underestimated how bright that would be," Rodney said in an undertone as he squinted at the swirling anomaly.

"You're absolutely positive this is going to work?" Sheppard still looked apprehensive.

"Yes, yes." The scientist said absently, completely absorbed in the figures that were being displayed on his laptop screen. "Good, the reactor is running at one hundred percent efficiency."

The other Sheppard approached the anomaly and stretched out a hand. "This is really cool." Rodney snorted. In his opinion it went way beyond 'cool'. "So what do I do?"

Rodney pointed at the aperture, "Just step through and in no time you'll be back where you belong."

"And with the people I belong with." The other Sheppard said knowingly as Rodney tried to ignore the odd sensation in his stomach. But Rodney noticed that the other man also looked slightly awkward, perhaps he wasn't as okay with his mistake as he tried to pretend. "Thanks for helping me out, both of you. Maybe we'll run into each other again sometime."

"I extremely doubt that." Rodney said, but his words were ignored as his Sheppard wished the other man good luck.

"Nice guy," Sheppard remarked as his double disappeared into the glowing white light. "It was nice to talk to someone who really gets me."

Rodney made a small 'hmpf' noise at this, but John ignored him. Glancing down at his laptop Rodney said, "According to these readings he should be back in his own universe now. I'm going to cut power." As the machine shut down, the lab was once again quiet. Sheppard was already in the doorway by the time Rodney joined him for the walk to the control tower to let Colonel Carter know that their guest was safely home.

John spoke first, "We actually traced back our lives, just to compare. Turns out they're virtually identical."

"I think he may have left some things out." Rodney had meant to say it casually, but it came out more as an accusation.

Sheppard stopped walking and turned to his friend. "What does that mean?" There was a fire behind his eyes. He was clearly ready to defend his alternate self.

"Let's just say that you two have different tastes." Rodney offered in what he hoped was a dismissive manner.

The pilot's eyes narrowed. "I don't follow, McKay."

"Well, maybe you didn't know him as well as you think. Can we just leave it at that?"

"No," Sheppard replied, his curiosity rising. He asked in a much gentler tone, "What do you know?"

"Nothing… I mean, if he didn't tell you then he obviously didn't want you to know. So I... I really shouldn't, I mean it's his – "

"Spit it out McKay!" Sheppard half-screamed at him.

Seeing no way around it, and extremely grateful that they were alone in the hallway, Rodney answered, "He's gay."

John did a double take and then started to laugh. "I thought you knew me well enough to know when I'm joking."

"You – he," Rodney stammered, "Was most definitely _not_ joking."

"C'mon Rodney, that guy he couldn't be..." Sheppard's voice was full of disbelief.

"Oh yeah, and I suppose heterosexual men always go around kissing one another do they?" He hadn't meant to tell him, but there it was all out in the open.

Eyes wide, Sheppard said, "He didn't!"

"Oh yes and it isn't something I'll be forgetting anytime soon. And not because it was pleasant I tell you."

Sheppard stood stunned for a moment. "But why did he…" he faltered, "you know." He finished, his face screwed up into a half-amused half-appalled look.

And there it was. Rodney blew out a long sigh. "Just remember that you asked," he began. He paused, considering the best way to phrase it. "He said that you and I… I mean, him and his Rodney they are kinda of in a..." he gestured frantically, trying to tell John without actually saying it. "You know a, relationship." He winced as soon as he had voiced it. The entire thought was just too bizarre.

If Sheppard had been shocked before it was nothing to the look on his face now. But after a few moments it was replaced by a thoughtful look. "Technically, wouldn't kissing you be cheating on his Rodney?"

It was Rodney's turn to be taken aback. "I guess so, technically. Maybe he wasn't worried about it, because we are sort of the same person." He studied Sheppard, but he had regained his normal calm demeanor. "Aren't you just a little freaked out about the thought of us in a relationship?"

"It's not _us_ Rodney. You're talking a completely different universe."

"Yes strictly speaking" he rolled his eyes, "but still, who would have ever thought that a reality like that could ever exist?"

"Hey, anything's possible." Sheppard starting walking once again, leaving Rodney standing thunderstruck, "Besides we _do_ make a pretty good team."

The End

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**A/N: So what do you think? Come on, I know you are just dying to hit that pretty little blue button.**


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